The purpose of this study is to quantitatively analyze the effect of an ectopic beat on heart rate variability (HRV) in the time domain, frequency domain, and in a non-linear analysis. A quantitative analysis was carried out by generating artificial ectopic beats that probabilistically contained a missed beat or a false-detected beat, and the statistical significance was evaluated though a comparison with an ectopic-free HRV by increasing the ratio of the ectopic beat in 0.1% increments from 0 to 50%. The effect of the interpolation on the ectopic HRV was also investigated by applying nearest-neighbor interpolation, linear interpolation, and cubic spline interpolation. The results confirmed a statistically significant difference (P < 0.05) even in the less-than-1% ectopic HRV in every domain. When interpolation was applied, there were differences according to the interpolation method used, but statistical significance was secured for an ectopic beat ratio from 1 to 2% to several tens of a percent. In the effect, linear interpolation, and spline interpolation were confirmed to have a higher effect on the high-frequency related HRV variables, and nearest-neighbor interpolation had a higher effect on low-frequency related variables.